This application addresses broad Challenge Area (04) Clinical Research, and specific Challenge topic 04-GM-101: Personalized drug response and toxicity. The Challenge and Potential Impact: With a global incidence of 1,151,298 each year, breast cancer is the most frequently diagnosed cancer and the second leading cause of cancer death (465,000/year) in women. Triple-negative breast cancer (TNBC), defined by lack of expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2), accounts for 15-20% of all breast cancers and is associated with poor clinical outcome, in part due to the lack of available targeted treatments. Currently, there is no consensus regarding optimal chemotherapy regimens for the treatment of such patients. Preclinical data suggests that TNBC may be sensitive to platinum-based chemotherapy because of deficiencies in BRCA-associated DNA repair, especially defective homologous recombination. We therefore hypothesize that gene expression changes will be identified in locally advanced triple negative breast cancer patients which are associated with pathological and/or clinical complete response to platinum-based chemotherapy. The aim of this study is to evaluate gene expression profiles and/or copy number variation associated with pathologic (pCR) and clinical complete response (cCR), in patients with TNBC treated with neoadjuvant platinum-based chemotherapy, in order to identify robust biomarkers for response prediction. The Approach: In order to address this challenge, we retrospectively reviewed 674 patients with locally advanced breast cancer (LABC) who received neoadjuvant chemotherapy between January 1999 and June 2008 at the University of Miami Sylvester Comprehensive Cancer Center/Jackson Memorial Hospital. Of these, 125 (18.5%) patients had histopathologic confirmation of TNBC. All patients received neoadjuvant platinum salts. Pathologic complete response (pCR) was strictly defined as no residual invasive disease in breast and axilla. RFS and OS estimates were calculated according to Kaplan-Meier (K-M) analysis. Patient demographics indicate a median age of 50 years (range 28-86 years), 60% premenopausal, 54% Hispanic, 34% African descent, and the remainder Caucasian. The TNM stage distribution at presentation: T1 0.9%, T2 5.2%, T3 53.4%, T4 40.5%, N0 25.0%, N1 36.2%, N2 35.4%, N3 3.4%, M0 100%, inflammatory breast cancer 11%, median tumor size = 9.5cm. Follow up duration ranged from 0.2 to 8.9 years. pCR was observed in 42 of 125 patients (34%;95% CI 26-42%). Median RFS by K-M analysis has not yet been reached in the subgroup of patients achieving a pCR, while the median RFS for non-pCR was 2.6 years (P=0.0002). Moreover, patients achieving pCR had significantly higher OS (median OS not reached vs. 5.1 years, pCR vs. non-pCR, respectively;P=0.001). To date, this is the largest reported single institution cohort of locally advanced TNBC uniformly treated with platinum-based chemotherapy regimens. In order to test our hypothesis, we will complete the following specific aims: Aim I: Identify genome-wide differences in gene expression between pathological complete responders and non-responders in locally advanced triple negative BC samples. Aim 2: Identify genome-wide differences in gene expression between clinical complete responders and nonresponders among locally advanced triple negative BC samples from patients which do not exhibit pCR. Aim 3: Investigate possible chromosomal alterations associated with gene expression differences. The use of expression array technology historically has been dependent upon the availability of intact RNA from fresh frozen tumor tissue for analysis, thus study of the many large retrospective cohorts with annotated clinical follow-up has not been possible. However, using an innovative approach we have recently successfully tested novel array probes specifically designed to detect partially degraded RNA from FFPE breast tumor material from samples at the University of Miami. The use of a probeset with extreme 3'sequence mitigates this previous technical limitation, and thus is considered highly innovative. Importantly, integration of high density array CGH technology with the expression array data is novel (to our knowledge, the first study in a well characterized platinum-treated locally advanced triple negative breast cancer cohort). This approach will allow identification of specific copy number variations and loss of heterozygosity, and their relation to gene expression changes. Our eventual goal will be to develop further understanding of biology of disease, and develop predictive biomarkers, for effective treatment for the subgroup of TNBC, who otherwise have poor prognosis. PUBLIC HEALTH RELEVANCE: With a global incidence of 1,151,298 each year, breast cancer is the most frequently diagnosed cancer and the second leading cause of cancer death (465,000/year) in women. Triple-negative breast cancer (TNBC), defined by lack of expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2), accounts for 15-20% of all breast cancers and is associated with poor clinical outcome, in part due to the lack of available targeted treatments. Currently, there is no consensus regarding optimal chemotherapy regimens for the treatment of such patients. Preclinical data suggests that TNBC may be sensitive to platinum-based chemotherapy because of deficiencies in BRCA-associated DNA repair, especially defective homologous recombination. We therefore hypothesize that gene expression changes will be identified in locally advanced triple negative breast cancer patients which are associated with pathological and/or clinical complete response to platinum-based chemotherapy. The aim of this study is to evaluate gene expression profiles and/or copy number variation associated with pathologic (pCR) and clinical complete response (cCR), in patients with TNBC treated with neoadjuvant platinum-based chemotherapy, in order to identify robust biomarkers for response prediction